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"Marine Traffic Simulation System" has been developed by the first author and others for long years. It has three simulation modes. First mode is normal navigation mode. It reproduces realistic traffic flows according to the predefined planed route. Second mode is collision avoidance mode. It has the feature of automatic collision avoidance for all ships besides the normal navigation mode. Third mode is external data mode. It reproduces traffic flow according to the data given by such as AIS. With collision avoidance mode, more realistic traffic flow can be reproduced. However, the validation of the simulation result is not yet done, because it was difficult to get the real traffic flow data before AIS data acquisition system established. This is one of the main purposes of this paper. The system is applied for southward area from Tokyo Bay. Assuming external mode as a real traffic flow, other two modes are evaluated. Normal navigation mode overestimates the navigational risk, while collision avoidance mode reproduces it fairly well in terms of several indices to represent the risk of the area. Three indices; number of occurrence of CR≧0.9, near-miss, and collision respectively, are proposed to assess the navigational risk and discussed. The normalization of these indices, traffic density and gaming area is also proposed and verified including the simulation results of two other areas.